vcf2msa
Conversion of a multi-sample VCF file to a multiple sequence alignment in FASTA format using htslib
Compilation:
make
Usage
./vcf2msa <reference fasta> <vcf>
output: within the current directory, saves a fasta file per sample contained in the VCF file.
ie. if the VCF file contains samples S1
, S2
, and S2
, S1.fa
, S2.fa
and S3.fa
will be produced.
The concatenation of these fasta files is the multiple sequence alignment.
TODO:
check name of input sequence against the sequence name associated with each VCF record- output the reference sequence as part of the MSA
- check that the input VCF is sorted
- output one fasta file instead of multiple fasta files?
- support nested variants
- support subsetting of samples (currently does the MSA for ALL samples)
- support or ignore complex variants, ie.
<CNV>
,<DUP>
, etc.